Dynalign protocols

View Dynalign computational protocol

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Dynalign specifications

Information


Unique identifier OMICS_20023
Name Dynalign
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Two sequences.
Output data A sequence alignment and a common structure for the two input sequences.
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


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Maintainer


  • person_outline Douglas Turner <>

Additional information


Dynalign is fully incorporated into the RNAstructure package.

Publication for Dynalign

Dynalign in pipelines

 (5)
2013
PMCID: 3691524
PMID: 23621982
DOI: 10.1186/1471-2105-14-142

[…] alignment and fold structure simultaneously. excessive computational resources (o(n6)) are required by the sankoff algorithm for a large-scale problem. some implementations of this approach, such as dynalign [], foldalign [], locarna [] and conan [], attempt to restrict its solution space by limiting the number of possible sub-structures. however these methods are still computationally expensive […]

2009
PMCID: 2659441
PMID: 19343219
DOI: 10.1371/journal.pcbi.1000338

[…] to contain an rna motif by qrna., we thank stefan washietl for insightful discussion on the svm model in rnaz. we also thank zizhen yao and andrew uzilov for discussions about using cmfinder and dynalign+libsvm., the authors have declared that no competing interests exist., this work was supported by department of energy grant de-fg02-05er63972 to gds. the funders had no role in study […]

2009
PMCID: 2709569
PMID: 19429694
DOI: 10.1093/nar/gkp276

[…] rnase p database (). the dataset is the same dataset that was utilized in benchmarking experiments performed in a previous paper (), so results are directly comparable with previous benchmarks on dynalign (), foldalign (), stemloc (), consan (), locarna () and single sequence structure prediction based on free energy minimization (). the cluster analysis was performed on the generated sample […]

2007
PMCID: 1868766
PMID: 17445273
DOI: 10.1186/1471-2105-8-130

[…] the exact alignment is constrained. highly probable nucleotide alignments, exceeding a specified threshold, are forced to occur in the simultaneous prediction of the alignment and common sequence., dynalign [,] is an implementation of the sankoff algorithm that predicts the lowest free energy structure common to two sequences. to make the calculation time tractable, a restriction […]

2007
PMCID: 1868766
PMID: 17445273
DOI: 10.1186/1471-2105-8-130

[…] sequences. since these require significantly more time than the shorter trna sequences the overall impact of the speed-up is very significant and in fact increases the length of sequences on which dynalign can be deployed., the memory requirements for the two methods are compared in table , where the minimum, maximum, and average memory (in megabytes) required for the 100 sequence pairs […]


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Dynalign in publications

 (29)
PMCID: 5712110
PMID: 29197323
DOI: 10.1186/s12864-017-4309-y

[…] in terms of run-time and memory usage for any practical use. to circumvent this problem, restricted, approximated or alternative versions of the sankoff-style algorithm, including foldalign [–], dynalign [–], cmfinder [], locarna [, ], murlet [], raf [] and dafs [], have been published with/without application to ncrna discovery. however, these methods are still too slow to perform […]

PMCID: 5382675
PMID: 28383059
DOI: 10.1038/srep46070

[…] stability in terms of z-score and structure conservation index (sci) to identify thermodynamically stable and evolutionary conserved rna secondary structures, respectively. dynalign ii, an update of dynalign, is a software package for prediction of the common secondary structure of two rna homologs by predicting inserted domains into dynamic programming algorithm. however, a major shortcoming […]

PMCID: 5067832
PMID: 27463680
DOI: 10.1089/nat.2016.0619

[…] that iav vrna loops can be targets for therapeutics, including asos., the vrna8 of influenza a/california/04/2009 (h1n1) was folded by comparison to vrna8 of a/vietnam/1203/2004 (h5n1) with the dynalign program [] in the rnastructure 5.4 package of software. dynalign finds the lowest free energy sequence alignment and secondary structure common to two previously unaligned sequences. folding […]

PMCID: 5444242
PMID: 26984616
DOI: 10.1093/bib/bbw022

[…] better. with decreasing sequence identity, their performance degrades more gracefully overall. shows the effect of smoothing on two of the curves. the green (foldalign), purple (pmcomp) and brown (dynalign) curves represent the three best performing plan b approaches. to a varying degree, they show a decline in the area between 60–40% identity, whereas their performance improves […]

PMCID: 4762127
PMID: 26942214
DOI: 10.1007/s41048-015-0001-4

[…] above limitations, several hybrid algorithms that combine free energy minimization and sequence comparison have been developed (mathews and turner ; havgaard et al. ; bernhart et al. ). for example, dynalign (mathews and turner ) combines free energy minimization and comparative sequence analysis to find a low free energy structure common to two sequences without requiring any sequence identity. […]


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Dynalign institution(s)
Department of Chemistry, University of Rochester, Rochester, NY, USA
Dynalign funding source(s)
Supported by NIH grant GM22939. D.H.M. is a trainee in the medical scientist training program, NIH grant 5T32 GM07356.

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